Exception in `docs/notesbooks/03-ODE-prototyping.ipynb`

[david-zwicker]

I tried running the notebook docs/notesbooks/03-ODE-prototyping.ipynb, which failed with the following error:

TypeError                                 Traceback (most recent call last)
Cell In[5], [line 43](vscode-notebook-cell:?execution_count=5&line=43)
     42 try:
---> [43](vscode-notebook-cell:?execution_count=5&line=43)     return self.interaction(u, lib)
     44 except TypeError:

Cell In[5], [line 23](vscode-notebook-cell:?execution_count=5&line=23)
     22 if self.interaction is None:
---> [23](vscode-notebook-cell:?execution_count=5&line=23)     self.interaction = lambda u, lib=None: u[0] * u[1]**2

TypeError: 'int' object is not subscriptable

During handling of the above exception, another exception occurred:

TypeError                                 Traceback (most recent call last)
Cell In[7], [line 4](vscode-notebook-cell:?execution_count=7&line=4)
      1 from evoxels.utils import rhs_convergence_test
      3 precision = 'float6[4](vscode-notebook-cell:?execution_count=7&line=4)'
----> 4 dx, errors, slope, order = rhs_convergence_test(
      5         ODE_class      = CoupledReactionDiffusion,
      6         problem_kwargs = {"D_A": 1.0, "D_B": 0.5},
      7         test_function  = test_funs,
      8         convention     = 'cell_center',
      9         dtype          = precision
     10     )
     12 print(f"Grid spacing: {dx}")
     13 print(f"Errors c_a:   {errors[0]}")

File [...]/evoxels/utils.py:101, in rhs_convergence_test(ODE_class, problem_kwargs, test_function, mask_function, convention, dtype, powers, backend)
     98 u = vg.bc.trim_boundary_nodes(u)
    100 ODE = ODE_class(vg, **problem_kwargs)
--> [101]([...]/evoxels/utils.py:101) rhs_numeric = ODE.rhs(0, u)
    103 if n_funcs > 1 and mask is not None:
    104     rhs_analytic = ODE.rhs_analytic(0, test_functions, mask_function)

Cell In[5], [line 68](vscode-notebook-cell:?execution_count=5&line=68)
     54 r"""Two-component reaction-diffusion system
     55 
     56 Use batch channels for multiple species:
   (...)     65     Backend array of the same shape as ``u`` containing ``du/dt``.
     66 """
     67 print(u)
---> [68](vscode-notebook-cell:?execution_count=5&line=68) interaction = self._eval_interaction(u, self.vg.lib)
     69 u_pad = self.pad_bc(u)
     70 laplace = self.vg.laplace(u_pad)

Cell In[5], [line 45](vscode-notebook-cell:?execution_count=5&line=45)
     43     return self.interaction(u, lib)
     44 except TypeError:
---> [45](vscode-notebook-cell:?execution_count=5&line=45)     return self.interaction(u)

Cell In[5], [line 23](vscode-notebook-cell:?execution_count=5&line=23)
     21 self._fourier_symbol = - max(self.D_A, self.D_B) * k_squared
     22 if self.interaction is None:
---> [23](vscode-notebook-cell:?execution_count=5&line=23)     self.interaction = lambda u, lib=None: u[0] * u[1]**2

TypeError: 'int' object is not subscriptable

This might be a simple problem with passing the wrong arguments, but I couldn't fix it quickly. In any case, it would of course be great if the supplied notebooks work out of the box.

[meyer-nils]

I can confirm this exception. Like in issue #39, the arguments for time and the solution variable seem to be swapped somewhere.

[daubners]

sorry my bad. between the submission in July and now, I've updated the scheme for ODEs to the more common (t, u) convention. All the notebooks have been updated in #41